It will be hard to implement since the "smallest tracking unit" is activity - a website or a window. I also can't see how to implement it without making everything too complex (the app's UX is too complex already in my opinion).
You can try to use a different browser since domains are bound to browsers. Like using productive Twitter in Safari and distracting Twitter in Opera.
So, I honestly wouldn't change anything about the interface, except to wrap the entire thing in an outer shell with something that represents what GTD software might call a context.
And depending on context, different rule sets apply. Anyway, that's just a suggestion, don't mean to stomp on your notion of product, what you've got is a great start and a neat coupling of product experience and interesting engineering!
I especially like the ambient info display in the app icon. Seeing whether the app is bordered in green or blue every time i tab up the app switcher is a great piece of design.